VMD-L Mailing List
From: M K (mahyar.karimi20_at_gmail.com)
Date: Tue Dec 16 2014 - 01:26:40 CST
I had visited this website before, which includes nice scripts available
What you want (and me too) is: "count_h-bonded_water_bridges" code.
The script looks nice. Thank to the developer :)
On Thu, Dec 11, 2014 at 10:57 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> Hi Mahdi,
> There are two options: if you use the GUI version of the h-bonds plugin,
> ask for the more detailed files. This has the problem that they are not
> resolved in time, and that is probably what you care about. If you don't
> use the GUI, (and this is the better alternative), you can the hbond
> interaction lists back as an output. Take a look at the documentation for
> the "measure hbonds" command (
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html), read it
> thoroughly, and then you can use the simultaneous list comparisons like
> Axel described.
> Basically, this is your pseudocode:
> -Make your selections (one each for protein, DNA, and water)
> -Iterate through your trajectory
> --update the frame each selection is using (eg. $sel frame $i)
> --get the list of hbond interactions at each frame (using measure hbonds
> repeatedly to catch all the different permutations)
> --check the lists that are returned to see if a water molecule appears to
> interact both with protein and DNA simultaneously.
> --write out your results to a file
> If you need help filling in the details, make a solid attempt first so we
> have code to work with, and then the list can make suggestions if
> -Josh Vermaas
> On 12/10/2014 04:33 PM, Mehdi Bagherpour wrote:
> ---------- Forwarded message ----------
> From: Mehdi Bagherpour <mehdi.bpour_at_gmail.com>
> Date: Wed, Dec 10, 2014 at 6:13 PM
> Subject: Re: vmd-l: How find water mediated hydrogen bond
> To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Dear Mr. Kohlmeyer,
> Thanks for your reply.
> The problem is in protein-water and DNA-water hydrogen bonding file that
> are computed by VMD, there are not any about address (Name, Chain, resid
> number ... ) of water molecules and we could not find which water atoms are
> interacted with both of them.
> On Wed, Dec 10, 2014 at 5:27 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> On Wed, Dec 10, 2014 at 10:40 AM, Mehdi Bagherpour
>> <mehdi.bpour_at_gmail.com> wrote:
>> > Dear All,
>> > I am going to find water mediated hydrogen bond between protein and DNA.
>> > Unfortunately when I get the hydrogen bond between water-protein or
>> > water-DNA, the address of water is not defined in VMD.
>> > Someone know how could I find the water atoms that are interacted (by
>> > H-Bond) between protein and DNA.
>> wouldn't it be sufficient to collect a list of water-protein and
>> water-dna hydrogen bonds and then compare which water oxygen atoms are
>> present in both lists?
>> > D --- W --- P ?
>> > kind regards,
>> > Mahdi
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.